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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-49110561-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=49110561&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 49110561,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000417901.6",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001199161.2",
"protein_id": "NP_001186090.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1384,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4155,
"cdna_start": 3946,
"cdna_end": null,
"cdna_length": 4721,
"mane_select": "ENST00000417901.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "ENST00000417901.6",
"protein_id": "ENSP00000395260.1",
"transcript_support_level": 1,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1384,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4155,
"cdna_start": 3946,
"cdna_end": null,
"cdna_length": 4721,
"mane_select": "NM_001199161.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3433C>A",
"hgvs_p": "p.Gln1145Lys",
"transcript": "ENST00000398888.6",
"protein_id": "ENSP00000381863.2",
"transcript_support_level": 1,
"aa_start": 1145,
"aa_end": null,
"aa_length": 1318,
"cds_start": 3433,
"cds_end": null,
"cds_length": 3957,
"cdna_start": 3752,
"cdna_end": null,
"cdna_length": 4559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3394C>A",
"hgvs_p": "p.Gln1132Lys",
"transcript": "ENST00000398896.6",
"protein_id": "ENSP00000381870.3",
"transcript_support_level": 1,
"aa_start": 1132,
"aa_end": null,
"aa_length": 1268,
"cds_start": 3394,
"cds_end": null,
"cds_length": 3807,
"cdna_start": 3587,
"cdna_end": null,
"cdna_length": 4366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001389594.1",
"protein_id": "NP_001376523.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1421,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 3946,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001389595.1",
"protein_id": "NP_001376524.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1421,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 3946,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001400288.1",
"protein_id": "NP_001387217.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1421,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 4234,
"cdna_end": null,
"cdna_length": 5043,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "ENST00000692912.1",
"protein_id": "ENSP00000508993.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1421,
"cds_start": 3742,
"cds_end": null,
"cds_length": 4266,
"cdna_start": 3946,
"cdna_end": null,
"cdna_length": 4755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3739C>A",
"hgvs_p": "p.Gln1247Lys",
"transcript": "NM_001351100.2",
"protein_id": "NP_001338029.1",
"transcript_support_level": null,
"aa_start": 1247,
"aa_end": null,
"aa_length": 1420,
"cds_start": 3739,
"cds_end": null,
"cds_length": 4263,
"cdna_start": 3943,
"cdna_end": null,
"cdna_length": 4752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3736C>A",
"hgvs_p": "p.Gln1246Lys",
"transcript": "NM_001199160.2",
"protein_id": "NP_001186089.1",
"transcript_support_level": null,
"aa_start": 1246,
"aa_end": null,
"aa_length": 1419,
"cds_start": 3736,
"cds_end": null,
"cds_length": 4260,
"cdna_start": 3940,
"cdna_end": null,
"cdna_length": 4749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3736C>A",
"hgvs_p": "p.Gln1246Lys",
"transcript": "ENST00000434032.6",
"protein_id": "ENSP00000401197.2",
"transcript_support_level": 2,
"aa_start": 1246,
"aa_end": null,
"aa_length": 1419,
"cds_start": 3736,
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"cds_length": 4260,
"cdna_start": 3948,
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"cdna_length": 4677,
"mane_select": null,
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"feature": null
},
{
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"aa_alt": "K",
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3733C>A",
"hgvs_p": "p.Gln1245Lys",
"transcript": "NM_001389602.1",
"protein_id": "NP_001376531.1",
"transcript_support_level": null,
"aa_start": 1245,
"aa_end": null,
"aa_length": 1418,
"cds_start": 3733,
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"cds_length": 4257,
"cdna_start": 3937,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3697C>A",
"hgvs_p": "p.Gln1233Lys",
"transcript": "NM_001389603.1",
"protein_id": "NP_001376532.1",
"transcript_support_level": null,
"aa_start": 1233,
"aa_end": null,
"aa_length": 1406,
"cds_start": 3697,
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"cds_length": 4221,
"cdna_start": 3901,
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"cdna_length": 4710,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3697C>A",
"hgvs_p": "p.Gln1233Lys",
"transcript": "ENST00000306026.6",
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"cdna_start": 3896,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3691C>A",
"hgvs_p": "p.Gln1231Lys",
"transcript": "NM_001389601.1",
"protein_id": "NP_001376530.1",
"transcript_support_level": null,
"aa_start": 1231,
"aa_end": null,
"aa_length": 1404,
"cds_start": 3691,
"cds_end": null,
"cds_length": 4215,
"cdna_start": 3895,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3748C>A",
"hgvs_p": "p.Gln1250Lys",
"transcript": "NM_001389596.1",
"protein_id": "NP_001376525.1",
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"cdna_start": 3952,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3745C>A",
"hgvs_p": "p.Gln1249Lys",
"transcript": "NM_001400290.1",
"protein_id": "NP_001387219.1",
"transcript_support_level": null,
"aa_start": 1249,
"aa_end": null,
"aa_length": 1385,
"cds_start": 3745,
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"cdna_start": 3949,
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"cdna_length": 4724,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001351101.2",
"protein_id": "NP_001338030.1",
"transcript_support_level": null,
"aa_start": 1248,
"aa_end": null,
"aa_length": 1384,
"cds_start": 3742,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 25,
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"exon_count": 27,
"intron_rank": null,
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"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys",
"transcript": "NM_001400292.1",
"protein_id": "NP_001387221.1",
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"mane_select": null,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3739C>A",
"hgvs_p": "p.Gln1247Lys",
"transcript": "NM_001389604.1",
"protein_id": "NP_001376533.1",
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},
{
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"strand": false,
"consequences": [
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],
"exon_rank": 25,
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"intron_rank": null,
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"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3736C>A",
"hgvs_p": "p.Gln1246Lys",
"transcript": "NM_001389598.1",
"protein_id": "NP_001376527.1",
"transcript_support_level": null,
"aa_start": 1246,
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"aa_length": 1382,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3736C>A",
"hgvs_p": "p.Gln1246Lys",
"transcript": "NM_001400293.1",
"protein_id": "NP_001387222.1",
"transcript_support_level": null,
"aa_start": 1246,
"aa_end": null,
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"cds_start": 3736,
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"cdna_start": 4228,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
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{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "c.3388C>A",
"hgvs_p": "p.Gln1130Lys",
"transcript": "XM_047447353.1",
"protein_id": "XP_047303309.1",
"transcript_support_level": null,
"aa_start": 1130,
"aa_end": null,
"aa_length": 1266,
"cds_start": 3388,
"cds_end": null,
"cds_length": 3801,
"cdna_start": 3592,
"cdna_end": null,
"cdna_length": 4367,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "n.91C>A",
"hgvs_p": null,
"transcript": "ENST00000483667.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"hgvs_c": "n.3433C>A",
"hgvs_p": null,
"transcript": "ENST00000693111.1",
"protein_id": "ENSP00000509474.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP19",
"gene_hgnc_id": 12617,
"dbsnp": null,
"frequency_reference_population": 0.0000020523148,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205231,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2751739025115967,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.167,
"revel_prediction": "Benign",
"alphamissense_score": 0.1401,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.589,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000417901.6",
"gene_symbol": "USP19",
"hgnc_id": 12617,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3742C>A",
"hgvs_p": "p.Gln1248Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}